X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.h;h=7316d508dd52729c8ddec87c34a08c76586cd4d1;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=d4f71abb9511b71f96fbdd4cbc11b080117db364;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650;p=mothur.git

diff --git a/parsimony.h b/parsimony.h
index d4f71ab..7316d50 100644
--- a/parsimony.h
+++ b/parsimony.h
@@ -13,24 +13,30 @@
 
 #include "treecalculator.h"
 #include "treemap.h"
-#include "globaldata.hpp"
 
 /***********************************************************************/
 
 class Parsimony : public TreeCalculator  {
 	
 	public:
-		Parsimony(TreeMap* t) : tmap(t) {};
+		Parsimony() {};
 		~Parsimony() {};
-		EstOutput getValues(Tree*);
-		EstOutput getValues(Tree*, string, string) { return data; };
+		EstOutput getValues(Tree*, int, string);
 		
 	private:
-		GlobalData* globaldata;
-		Tree* copyTree;
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+	
 		EstOutput data;
-		TreeMap* tmap;
-		map<string, int>::iterator it;
+		int processors;
+		string outputDir;
+	
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, TreeMap*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, TreeMap*);
 };
 
 /***********************************************************************/